IMC INDEX Functions Structured List = IMC HELP Structure

Last Modified: 2013-08-15 (木) 14:33:19

This page has no corresponding page in Japanese.

3 IMC Primer

30: Structure of IMC Main Window

31: How to Launch IMC

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32: How to Terminate IMC

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33: How to check whether a new IMC version is available for downloading

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34: Load Sequence Files

341: Load Nucleotide Sequence Files

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  • 341A: Load Un-annotated Sequence(s)
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  • 341B: Load Annotated Sequence(s)
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342: Loading and saving of amino acid sequences

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343: Change the Genetic Table

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344: Load Sequences in the Multiple Genome Viewer

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345: Automatic Determination of Sequence Type

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35: Main Window Structure and Reference Feature Map

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36: Basic Operation of the Feature Map

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361: Change the Feature Layout Style

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362: Browse the Content of a Feature

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363: Select a region in the main feature map

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364: Select nucleotide sequences on the sequence lane

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365: Select Feature(s)

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37: Print the main feature map

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38: IMC Menu and the Tool Box

381: Menu, tool button and functions

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  • 381A: FILE menu
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  • 381B: EDIT menu
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  • 381C: VIEW menu
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  • 381D: SEARCH menu
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  • 381E: MOVE menu
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  • 381F: OPTION menu
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  • 381G: TOOLS menu
  • 381H: CLONING menu
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  • 381I: GENOME ANALYSIS menu
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  • 381J: ARRAY ANALYSIS menu
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  • 381K: HELP menu
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382 Remove the Button Tool Box

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383 Showing / hiding single tool buttons

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384 Button Arrangement Differences between IMC Editions

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385 Popped Up Menus by Mouse Right Button Click

  • 385A: Right button click on a feature on MFM
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  • 385B: Popup menu on the selected region of the main feature map
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  • 385C: Menu popped up from a deleted feature on the MFM
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  • 385D: Popup menu on a sequence icon in the reaction tube
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  • 385E: Right button menu on a feature on the reference feature map
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  • 385F: Popup menu on a sequence icon in the reference tube
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  • 385G: Popup menu on the selected sequence on the main feature map
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39: HELP

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391: Help Overviews

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392: Initial Download of the HELP files

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393: Update HELP

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394: Change Language

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395: See Index

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396: Expansion and Folding of HELP Contents

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A: Features and the Feature Map

A01: Reaction tube, or sequence loading pool

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A01A: Loading in the reaction tube and switching of the feature map

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A01B: Remove the sequence icon from the reaction tube

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A02: Feature Map

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A02A: Scrolling, Zooming and Jumping the Map

  • A02A1: Scrolling the main feature map
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  • A02A2: Change the scroll step size
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  • A02A3: Zooming the main feature map
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  • A02A4: Change the zoom magnification factor
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  • A02A5: Operation of the line cursor
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  • A02A6: Jump to a new position or region of the feature map
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A02B: Customization of the main feature map

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  • A02B1: Zooming rate and scroll size of the main feature map
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  • A02B2: Label setting
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  • A02B3: Set figure of a feature key
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  • A02B4: Set color of a feature key
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  • A02B5: Assign a texture pattern to a feature
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  • A02B6: Draw a short feature key on the sequence lane
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  • A02B7: Change the connection line type of joined features
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A02C: FLS: Feature Layout Style

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  • A02C1: Apply a feature layout style to the main feature map
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  • A02C2: Set an FLS as the default FLS
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  • A02C3: Save the modified style as a new layout style
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  • A02C4: Creation and deletion of FLS
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  • A02C5: FLS priority, default FLS and auto setting FLS
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  • A02C6: Preset FLS
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  • A02C7: Import an external FLS
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A02D: Print the main feature map

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  • A02D1: マップ描画パラメータ
  • A02D2: 用紙とページ設定
  • A02D3: 画像ファイル出力

A03: Lane

A03A: Basic Operation of Lanes

  • A03A1: Change the height of the lane
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  • A03A2: Move a lane
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  • A03A3: Temporal hiding of lanes
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  • A03A4: Add, edit and delete lanes
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A03B: Feature Lane

A feature lane is an area in the main feature map of IMC for graphical presentation of the biological features. Any number of feature lanes can be allocated in a feature map.

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  • A03B1: Show base number on a feature lane

    The base number of the current mouse position on a feature lane is displayed in red character. As the mouse moves, the number indicated is changing.

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  • A03B2: Layout style settings of a feature lane

    By using the Feature Layout Style (FLS), the feature map can be drawn with huge versatility. The number of feature lanes assigned to an FLS has no limit.

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  • A03B5: Left button click on a feature

    A left button click on a feature makes the feature color to its compliment color and paints the background color of corresponding nucleotide sequence in gray. The line cursor moves to be aligned with the feature.

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  • A03B6: Pop-up menu after right mouse click on a feature

    After a right mouse button click on a feature a menu pops up that provides various options applicable for the feature. Macintosh users apply Cmd key together with mouse click. From Version 4.1.35 all the menus are displayed. Previously only the menus that can be executed for the selected feature were displayed.

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  • A03B8: Show the feature contents on a balloon

    By moving the mouse over one of the features in a feature lane, the contents of the feature is displayed on a balloon.

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A03C: Content Profile Lane

A content profile lane is a region to draw profiles such as nucleotide content. One or more content profile lanes are assigned to any position of the feature map.

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  • A03C0: Sliding Window Approach

    The sliding window algorithm is used when computing the content profiles.

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  • A03C1: Layout style settings of a content profile lane

    Any number of content profile lanes can be assigned in one feature map.

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  • A03C2: Manual settings of upper/center/lower level lines

    The upper/center/lower line of a content profile lane can be set manually.

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  • A03C3: Change resolution and smoothness of profile graph

    The resolution and smoothness of a profile graph can be changed with the values of the window size and the step size parameters.

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  • A03C4: Change the colors of graph

    The colors of the content profile graph can be individually set. The upper level color is assigned between the upper level line to the center level line and the lower level color is assigned between the center level line and the lower level line.

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  • A03C5: Show content profi les such as GC content profi le

    A content profi le can be displayed in a content profi le lane. A content profi le is computed using the "Sliding Window" approach, and drawn as wide as the whole span of the sequence. The resolution and smoothness are adjustable by changing the parameters. A profi le is drawn in two different color, one for the upper region and another color for the lower region which are divided by the center line. A thinning out process is applied when drawing the profi le with minimal computing time.

    Such content profi les are also drawn in the circular genome map menu.

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  • A03C6: Show skew profi les such as GC skew profi le

    A skew profi le can be displayed in a content profi le lane. A skew profi le is computed using the "Sliding Window" approach, and drawn as wide as the whole span of the sequence.

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  • A03C7: Show cumulative skew profiles such as cumulative GC skew profi le

    A cumulative skew profi le can be displayed in a content profi le lane. A cumulative skew profi le is computed using the "Sliding Window" approach, and drawn as wide as the whole span of the sequence. The resolution and smoothness are adjustable by changing the parameters. A profi le is drawn in two different color, one for the upper region and another color for the lower region which are divided by the center line. A thinning out process is applied when drawing the profi le with minimal computing time.

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  • A03C8: Draw profile of arbitrary numeric data

    A content profile lane provides a function to draw a profile that is constructed from a series of numerical values. The data consist of three columns including the start and end position and the intensity value.

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  • A03C9: Fickett Profile
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A03D: アレイプロファイルレーン

  • A03D1: データのタイプ
  • A03D2: FLSの設定
  • A03D3: ストランド指定・オーバーレイ
  • A03D4: スケール設定
  • A03D5: 対数表示等
  • A03D6: アレイ発現ファイル指定
  • A03D7: アレイ間演算
  • A03D8: データ補正
  • A03D9: グラフ表示設定

A03E: Restriction Map Lane

The restriction enzyme recognition sites are drawn on the main feature map as "Restriction Enzyme Map" lanes.

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A03F: Sequence Lane

The sequence lane is the special lane to display a nucleotide sequence and its translation into amino acid sequences; only one lane in the main feature map can be assigned to this type. The sequence lane displays a nucleotide sequence of the forward strand on top of its complement sequence of the reverse strand, and also shows the amino acid sequences of the three frames of either strand. The sequences in the sequence lane can be scrolled horizontally by clicking the red arrow buttons on both sides of the sequence “scale” lane. Continuous scrolling is possible by keeping the button pressed. The scroll size of one click can be changed by the parameters.

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  • A03F1: Display the base position on the nucleotide sequence.

    On a sequence lane, the base position of the sequence can be displayed by moving the mouse. The position is counted from the fi rst base of the 5' upstream of the sequence as one.

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  • A03F2: Selection and Clear Selection of Nucleotide Sequences

    Selection and clear selection of nucleotide sequences are basic operations on the sequence lane.

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  • A03F3: Register the selected sequence as a new feature.

    The selected region can be registered as a new feature. For this purpose, the "Feature Registration" dialog is used.

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  • A03F4: Register the selected sequence as a new primer sequence.

    Any single selected sequence region can be registered as a new primer sequence. The "Primer Registration" dialog is used for the purpose. The registered primers can be listed on the "Primer List" window and can also be saved as a primer fi le.

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  • A03F5: Copy and paste of nucleotide sequence in a sequence lane

    Any region in the nucleotide sequence in a sequence lane can be copied to the clipboard and pasted in the sequence of the lane. Any copied nucleotide sequence that is copied by other applications such as an editor software, can be pasted onto the sequence (between two adjacent nucleotides or on the selected region of the nucleotides) in a sequence lane or the input field of "Input Direct Sequence" dialog.

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  • A03F6: Register the selected sequence as a sequence pattern.

    Selecting a span of sequence in a sequence lane can be registered as a new nucleotide pattern. The pattern is used for the pattern search.

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  • A03F7: Delete nucleotides in a sequence lane.

    A part of the nucleotide sequence in a sequence lane can be deleted. The features that are completely contained in the deleted nucleotides will be also deleted completely. The features that are partially overlapped may be modifi ed by the feature key names. As for the CDS features are shifted with the frames and the amino acid translations are also automatically changed.

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  • A03F8: Replace the selected nucleotides with other nucleotides.

    The selected nucleotides in a sequence lane can be replaced with different nucleotides. If there are overlapped features and the numbers of each nucleotide is different with each other, the frame will be automatically shifted and the amino acids are also changed. In addition, the stop codons may be also shifted.

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  • A03F9: Insert nucleotides between two nucleotides.

    Any nucleotides can be inserted between two nucleotides in a sequence lane. If there are overlapped features and the numbers of each nucleotide is different with each other, the frame will be automatically shifted and the amino acids are also changed. In addition, the stop codons may be also shifted.

    A nucleotide sequence with features is also inserted. In this case, all the features are also inserted.

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  • A03F10: Display features on the sequence of a sequence lane.

    Feature fi gures prepared for short feature keys can be displayed in the sequence of a sequence lane, as well as in the main feature map.

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  • A03F11: Amino acid presentation in sequence lane.

    In a sequence lane, if there are protein coding regions on the nucleotide sequence, the corresponding amino acid sequences are displayed along with the nucleotide sequence. If the On-Reaction-Tubeloaded sequence fi les of chromosomes or DNA fragments have "Qualifi er /translation=", the amino acid sequences are also displayed. If not, the amino acid sequences are not displayed.

    As for Prokaryotes, the fi rst amino acid is changed to M (Methionine). If the translation table is selected as Qualifi er /trans_table=XX, translation is performed according to the selected table. If no translation table is selected, translation is performed as it is "trans_table=1". Amino acid code used in IMC is one character code system, however its position in a codon in the both strands can be specified by users.

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  • A03F12: Change position of single character code of amino acid in codon.

    The amino acid codes can be displayed in a coding region in the sequence lane. The displaying code are one character codes and its position in codon is also user specifi ed per strand.

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  • A03F13: Change character color of nucleotide or amino acids code in the sequence lane.

    The colors of each nucleotide or amino acid code displayed in the sequence lane can be changed.

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  • A03F14: Display candidates of start and/or stop codon

    The candidates for start codon and/or stop codon can be displayed in the amino acids frames of the sequence lane.

    As for the same function in "Annotation Window", the setting method is different from the above setting. The "Annotation Window" has its own setting buttons in the Window itself.

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A03G: Sequence Ruler Lane

The sequence ruler is a rule for the nucleotide and amino acid sequence that are displayed in the sequence lane and the unit is nucleotide number that is counted from the first nucleotide of the sequence. The ruler can not be controlled by the user and is automatically set by system.

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A03H: Map Ruler Lane

Map ruler is displayed in the unit of nucleotide and spans the whole horizontal range of the main feature map. The ruler is automatically set and can not be control by users.

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A03I: Scroll Bar Lane

The scroll bar is used for moving the main feature map by fetching the blue triangle mark of the vertical line cursor. The scroll bar lane is a specially designed lane that accommodates triangle mark and vertical line cursor that indicates the sequence displaying region of the main feature map.

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A03J: LRGMレーン

A04: Feature

A04A: Add, delete and copy feature

A feature can be registered a new one on the currently loaded sequence. To delete or copy an existing feature can also be performed.

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  • A04A1: Set features as deleted

    Deletion of features are performed with two stages. In the fi rst stage, features are not deleted yet but are marked as deleted. In the second stage, all the delete-marked features can be actually and completely deleted. One single feature can be set as deleted as well as multiple features can be set as deleted at one operation. In addition, several search functions of IMC provide "delete" function against the hit features by each search result. Search functions that support "delete" function are "Feature Search", "Keyword Search" and "Classifi cation Search".

    Even the second stage is performed, the deleted features can be restored if the fi le that contained the features are not saved.

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  • A04A2: Delete the features actually A feature can not be actually only if the feature is set as deleted. To execute "delete feature completely" function is necessary to delete the feature actually. A few kinds of way to delete the "set as deleted" feature completely, are provided such as to delete the features one by one, to delete all the "set as deleted" features in a selected region or to delete all the "set as deleted" features.
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  • A04A3 Register a new feature (dragging in a sequence lane) Among the several methods to register a new feature, mouse dragging in a sequence lane is explained.
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  • 新規登録(フィーチャーマップ上)
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  • フィーチャー定義ファイルからの登録
  • 解析結果からの登録

A04B: フィーチャーの表示

A04C: Join Operation

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A04D: Feature Label

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A04E: Copy and Paste of Feature Sequences

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A04F: Change Feature Figure

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A04G: Color Presentation of Features

  • フィーチャーキー別に異なるカラーで描画する
  • 相同性スコア別にカラー表示
  • COG機能分類(Classification)別にカラー表示する
  • アノテーション段階(Category)別にカラー表示する
  • EC番号別にカラー表示する
  • 指定フィーチャーを特定のカラーで表示する
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A04H: Link Files to Feature

  • 複数の文献を一つのフィーチャーにリンクする
  • フィーチャーから直接文献を参照する
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A04I: Link 3D Structure File to Feature

  • 立体構造をフィーチャーから直接参照する
  • 立体構造ビューアのインストール
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A04J: フィーチャー定義のCSVファイル保存

A04K: Feature Fusion

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A04L: Feature Numbering

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  • フィーチャー定義ファイルインポート時に付加
  • ESTマッピング時に連番付加
  • アミノ酸配列マッピング時に付加
  • 検索ヒットフィーチャーに付加
  • 指定フィーチャーキーに付加
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A05: MGV多重ゲノムビューア(=参照ゲノムマップ)ローディングリストとフィーチャーレーン

  • A05A: 多重ゲノムビューアへのゲノム配列ロード
  • A05B: 横スクロール
  • A05C: 連動ズーム
  • A05D: 独立ズーム
  • A05E: 追加読込
  • A05F: 一部ゲノム除去
  • A05G: 表示順序を変更
  • A05H: 相同性検索の実行と遺伝子アラインメント
  • A05I: 他の機能からの連動
  • A05J: 印刷する

A06: Feature Key

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A07: Feature Export

  • BED形式

A08: Feature Import

  • インポートされるファイル形式自動判定
  • CSV-A
  • CSV-B
  • CSV-C
  • XanaGenome
  • Glimmer
  • 旧GenomeGAMBLER形式
  • tRNAScan-SE
  • GeneScan?
  • JSNP
  • GFF
  • GTF
  • Blast結果ファイル
  • AUGUSTUS
  • BED
  • dbSNP
  • RNAmmer

A09: Feature Mapping

A10: Database Handling

A11: Color Settings, Common Operations

A12: Printing, Common Operations

B: File Handling

B01: 核酸配列ファイルの操作

B01A: GenBank/EMBL形式ファイルの操作

  • GenBank/EMBL形式塩基配列ファイルの保存と相互変換
  • FastA形式塩基配列ファイル
  • テキスト形式塩基配列ファイル
  • 数字・空白文字を含む塩基配列ファイル
  • シーケンシングファイル(ABI・SCFファイル)

B01B: 編集済ファイルの自動保存の確認メッセージ表示指定

B01C: 任意領域塩基配列をFastA形式で保存する

B01D: 保存するGenBankファイルの拡張子を変更する

B01E: 保存するGenBankファイルから指定したfeature KeyやQualifierを取り除く

B02: アミノ酸配列ファイルの操作

B02A: アミノ酸配列読み込み

B02B: アミノ酸配列の保存

C: 編集

C01: Copy

C02: Paste

C03: Delete

C04: Restore

C05: Select

C06: Numbering

C07: Filtering

D: View

D01: GenBank/EMBL File Browser

  • GenBank/EMBL File Viewerの起動
  • GenBank/EMBLファイルの内容の閲覧
  • フィーチャーマップとの連動

D02: Sequence Viewer

塩基配列ビューアは塩基配列と翻訳アミノ酸配列を表示するビューアです。

  • 塩基配列ビューアの画面の説明
  • 塩基配列ビューアを起動します。
  • 表示範囲を変更します。
  • 表示中の塩基配列の逆相補鎖を表示します。
  • 表示中の塩基配列を翻訳したアミノ酸配列を表示します。
  • 塩基配列の目盛を表示・非表示を切り替えます。
  • 塩基配列の目盛を相対番号とします。
  • 塩基配列の目盛を左側面・上方に表示します。
  • 1行に表示する塩基配列の数を変更します。
  • 塩基配列を印刷します。

D03: Array Profile Viewer

この機能はフィーチャーレイアウトスタイルのアレイプロファイルレーンに移動されました。

D04: Global Genome Rearrangement Map Viewer

D05: Local Genome Rearrangement Map Viewer

  • Local Genome Rearrangement Mapの機能と操作?

    ローカルゲノム再配置マップの表示には独立のウィンドウをもたず、メインフィーチャーマップのLGRMレーン上に描画されます。

D06: Plasmid Map Designer Viewer

D07: Venn Diagram Viewer

D08: Gene Expression Matrix Viewer

D09: Circular Genome Map Designer Previewer

  • Circular Genome Map Designer Previewer?
  • 機能と操作一覧?

D10: Multiple Genome Viewer

D11: Phylogenetic Tree Viewer

D12: Single Trace Viewer

  • Unified with Multiple Trace Viewer

D13: Multiple Trace Viewer

D14: Multiple Sequence Alignment Viewer

D15: Annotation Window

D16: Description Window

D17: DotPlot Viewer

D18: Codon Usage Viewer

D19: Print Preview

D20: Content Profile Viewer

E: Search

E00: Common Functions

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E00A: 複数配列に対する検索

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E00B: 検索結果核酸配列のファイル保存

E00C: 検索結果アミノ酸配列のファイル保存

E00D: 検索結果からのコドン使用頻度表示

E00E: 検索結果ダイアログからのフィーチャー削除

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E01: Feature Key Search

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Feature Key別にすべてのFeartueを検索し、結果としてそれらのFeatureの塩基配列上の位置や、Featureに付けられた注釈をリスト表示でき、かつそのリストから直接そのFeatureの位置のFeature Mapに移動表示できます。また、リストはCSVファイルとして出力できます。

E01A: Functions and Features

E01B: Restrictions?

E01C: Algorithms and Data Structure?

E01D: Operations?

E01E: Operations from FK Search Result Dialog?

E01F: Operations from Codon Usage Dialog?

  • フィーチャーキー検索機能概要
  • 登録フィーチャー数リストを表示
  • フィーチャーの塩基位置を表示
  • 選択されたフィーチャー情報をCSVファイル保存
  • 選択フィーチャー位置へジャンプ

E02: Keyword Search

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E02A: Overviews

E02B: Multiple Key Word Search(AND)

  • 2語以上のキーワードのAND検索を実行します。

E02C: Multiple Key Word Search(OR)

  • 2語以上のキーワードのOR論理検索をします。

E02D: Only Hit Features are viewed on the Feature Map

  • キーワード検索で検索されたフィーチャーだけをフィーチャーマップ上に表示することができます。
  1. フィーチャーマップに注釈付配列ファイルをロードしておきます。
    • 上記注釈ファイルのフィーチャーマップが表示されています。
  2. キーワード検索ボタン をクリックします。
    • 「Key Word Search」Dialogが表示されます。
  3. たとえば「kinase」と入力し、「Search」ボタン をクリックします。
    • 「kinase」にヒットしたフィーチャー数が表示されます。
  4. 「kinase」にチェックします。
    • 個々のエントリーが表示されます。
  5. すべてのエントリーにチェックする。あるいは「Select All」ボタン をクリックします。さらに、「Only Selected Feature(s) is displayed」ボタン をクリックします。
    • 「kinase」というキーワードをもつフィーチャーのみがフィーチャーマップ上に表示されます。
  6. 「Close」ボタンをクリックする。
    • 全フィーチャーが再度表示される

E02E: Key Word Search against Multiple Sequence Files

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E02F: Annotation Windows and Description Windows can be launched from some of search results list windows.

In previous versions, IMC users launches Annotaion Window or Description Window only by Clicking the target feature idons or clicking the selected region on the Main Feature Map. Four of search result list windows in IMC provide direct button to launche Annotation Window or Description Window.

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E02G: Set Classification value from search windows

This function is used for setting in block one specifi ed text value to the qualifi er "/classfi cation=" from the search result windows of "Statistics", "Feature Key Search" and "Key Word Search". The Classification codes, which are, in defaultl, mostly corresponding to the COG codes, are used to classify features by different color notations on the Feature Map, the Circular Genome Map or the Classifi cation Search.

The qualifier "/classification=" is originally created by in silico biology, inc. to classify the features by colors.

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E03: Sequence Pattern Search

  • パターン登録?
  • パターン検索?
  • パターン検索機能概要
  • 配列パターンを登録する
  • 塩基配列パターンを遺伝子間を検索対象領域として検索する
  • 遺伝子上のアミノ酸配列パターンを検索する
  • 配列パターンを登録せずにペーストしたパターンを検索する
  • 発見された配列パターンを新規配列パターンとして登録する
  • 発見された配列パターンの部位を新規フィーチャーとして一括登録する。

E04: Homology Search

  • E04A: 参照ゲノムマップ上のフィーチャーに対する検索
  • E04B: 参照ゲノムマップフィーチャーからの検索
  • E04C: 登録済みDBに対する検索
    • Blast検索用DBを作成する
    • 多数のDBを一つのDB名称で参照する
    • 登録DBに対する相同性検索の実行
    • 実行結果の参照
  • E04D: Batch Homology Search
  • E04E: Search via Internet
  • E04F: Search on External Server

E05: Restriction Enzyme Site Search

  • See Restriction Enzyme

E06: Priming Site Search

  • See PCR

E07: SNP Search

F: Move

  • F01: ズーム
  • F02: ジャンプ

G: Option Settings

G00: Overviews and Common Operations

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G01: Machine Dependent Options

G01A: Commands

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G01B: Proxy Server

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G01C: External Server

G02: Map Drawing

G02A: Feature Map

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G02B: Sequence Lane

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G02C: Reference Map

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G02D: Qualifier Order

G03: Color Settings

G03A: Classification Color

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G03B: EC Number Color

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G03C: Category Color

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G03D: Blast Result Color

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G04: File Settings

G04A: CSV Files

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G04B: Tree Expansion

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G04C: FastA Definitions

G05: Analysis Parameters

G05A: Genome Analysis

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G05B: Homology Search

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G05C: Repeat Detection

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G05D: Amino Acid Profiling

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G05E: VENN Diagram

G05F: Search Options

G05G: LGRM

G05H: SNP

G06: Cloning Options

G06A: Cloning

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G06B: PCR Primer Design

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G07: Sequence Operation Parameters

G08: Annotation Parameters

G08A: Filtering

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G08B: Annotation Transfer

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G08C: Description Window

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G09: Other Options

G09A: Lab Note

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G09B: Setup

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H: Assembling and Clustering

H01: de novo Assembling

H02: Viewing assemble results

H03: Input Sequences and Environments for Assembling

H04: RNA Clustring

I: Cloning

I00: Cloning Overviews

I01: Restriction Enzyme

  • I01A: 制限酵素機能の概要?
  • I01B: 制限酵素部位を見つける?
  • I01C: 制限酵素で配列を消化断片化する?
  • I01D: 消化断片のファイル保存
    • 消化断片リストのCSVファイル保存
    • 消化断片のFastAファイル保存
    • 消化断片のMultiple FastA保存
  • I01E: 制限酵素認識部位を新規フィーチャー登録する
  • I01F: 消化断片の一次元ゲル電気泳動結果表示
  • I01G: メチル化影響部位を表示する
  • I01H: インサートチェック用に最適な2種の制限酵素を見つける
  • I01I: 制限酵素の絞り込み
    • 対象塩基配列上に指定個数の制限部位をもつ制限酵素を選択する
    • 選択された制限酵素リストをさらに絞り込む
  • I01J: 制限酵素地図を描く
    • 別ウィンドウを開き、独立に描画
    • フィーチャーマップ上に 制限酵素地図レーンを追加設計する
  • I01K: 制限酵素による環状ベクター配列の開環
  • I01L: 制限酵素消化断片の末端処理
    • 末端形状表示
    • 末端平滑化
    • 脱リン酸化・リン酸化
  • I01M: 制限酵素を登録・管理する
    • 制限酵素を新規登録する
    • 制限酵素ファイルを入れ替える
    • 制限酵素の一部だけのセットを作成・参照する

I02: PCR Primer Design

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  • PCR Primer Design, Functions and Operations?
  • I02A: PCR Primer Management
  • I02B: Primer Modifications
    • Attach a recognition site of restriction enzyme
    • Attach a tag sequence
    • Add mutation
  • I02C: Manual Primer Design
  • I02D: Batch Primer Design
  • I02E: Whole Genome Primer Design
  • I02F: In-Fusion Primer Design

I03: PCR

  • PCRを実行する
  • プライミング部位を新規フィーチャーとして登録する
  • 複数の塩基配列を対象にPCR実行する
  • PCR産物をベクター配列にインサートする:TAクローニング
  • PrimerリストからPCR増幅される塩基配列ファイルをロードする

I04: Ligation

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IMC_I04_LigationEN? gbni_s.gif
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IMC_I04_LigationJP japan_s.gif
  • ライゲーション機能概要
  • 反応チューブ内にロードされている全塩基配列の末端形状の表示
  • 塩基配列末端の形状チェックの指定
  • 2つの塩基配列間のライゲーション反応
  • セルフライゲーションの実行
  • ライゲーション産物のファイル保存

I05: プラスミドマップ

  • プラスミドマップ描画機能概要
  • プラスミドマップの描画
  • プラスミドマップの描画スタイルの登録と参照

I06: Gel Electrophoresis

I07: 末端平滑化・リン酸化

  • 平滑化機能?

I08: TA Cloning

  • 環状ベクターの開環
  • プライマーの作成
  • PCR実行
  • ライゲーション反応
  • プラスミドマップで確認する

I09: インサートチェック最適酵素決定

  • ライゲーション反応の実行
  • 最適制限酵素の探索
  • ゲル電気泳動の表示

J: Genome Analysis

J00: Overviews

J01: Reverse Complement

  • 注釈付き塩基配列ファイルの逆相補鎖配列の生成
  • 逆相補鎖配列の保存
  • 配列切断と逆相補鎖生成の組み合わせによる比較用近縁種ゲノム整列のための編集

J02: Content Profile Analysis

  • 塩基組成の計算と表示機能
  • ゲノム全体にわたる塩基組成表示
  • 選択領域の塩基組成表示

J03: Codon Analysis

  • IMC_CodonUsage?
  • コドン使用頻度表機能の概要
  • フィーチャー単位のコドン使用頻度表
  • 選択領域にあるコドン使用頻度表
  • ゲノム上の全CDSのコドン使用頻度

J04: ORF Analysis

  • ORF解析機能の概要
  • 原核生物ORF同定Longest法

J05: Coding Region Translation

  • ORF候補のアミノ酸配列翻訳
  • CDS上のアミノ酸翻訳
  • 遺伝暗号表の選択

J06: Amino Acid Profile Analysis

K: Database Handling

K01: Blast検索用データベースの作成

K02: GenBank正規リリースファイルの系統樹展開

K05: TaxiSpiderを使った簡単配列取得

K06: iSpiderを使った自動データベース取得

L: Annotation

L01: Databases for Annotation

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&ref(): File not found: "IMC_.ja.pdf" at page "imcimgE"; japan_s.gif
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IMC_L01_EN? gbni_s.gif
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IMC_L01_JP? japan_s.gif

L02: 遺伝子同定ソフトウェア

L03: 一括相同性検索と注釈自動転記

L04: シーケンスビューアを使ったアノテーション

L05: Description Windowを使ったアノテーション

L06: Annotation Windowを使ったアノテーション

wiki
IMC_Annotation_Window?

L07: 注釈の整理・不要情報の除去

L08: DDBJ大量塩基配列登録ファイル生成機能

wiki
IMC_DDBJ_Masssubmission

M: Multiple Alignment

M01: 塩基配列アラインメント

M02: アミノ酸配列アラインメント

M03: 進化系統樹作成

M04: アラインメントファイルの保存

N: Whole Genome Analysis

N01: ゲノム内反復配列抽出

N02: Pathway Analysis

wiki
IMC_PathwayAnalysis?

O: Comparative Genomics

O01: Circular Genome Map

wiki
IMC_CircularGenomeMapEN?gbni_s.gif &lastmod(IMC_CircularGenomeMapEN);
IMC_CircularGenomeMap?japan_s.gif &lastmod(IMC_CircularGenomeMap);

O02: Multiple Genome Viewer (MGV = Reference Genome Map)

wiki
IMC_ReferenceGenomeMapEN?gbni_s.gif &lastmod(IMC_ReferenceGenomeMapEN);
IMC_ReferenceGenomeMap?japan_s.gif &lastmod(IMC_ReferenceGenomeMap);

O03: Dot Plot

wiki
IMC_DotPlotEN?gbni_s.gif &lastmod(IMC_DotPlotEN);
IMC_DotPlot?japan_s.gif &lastmod(IMC_DotPlot);

O04: VENN Diagram

PDF
fileIMC_O04.en.pdf gbni_s.gif
fileIMC_O04.ja.pdf japan_s.gif
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IMC_O04_VennDiagramEN gbni_s.gif 2013-05-07 (火) 17:31:31
IMC_O04_VennDiagramJP japan_s.gif 2013-05-07 (火) 17:31:25

O05: Extraction of the Unique Regions between two Genomes

O06: Global Genome Rearrangement Map

wiki
IMC_GlobalGenomeRearrangementMapEN? gbni_s.gif &lastmod(IMC_GlobalGenomeRearrangementMapEN);
IMC_GenomeRearrangementMap? japan_s.gif &lastmod(IMC_GenomeRearrangementMap);

O07: Local Genome Rearrangement Map

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fileIMC_O07.en.pdf gbni_s.gif
fileIMC_O07.ja.pdf japan_s.gif
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IMC_O07_LocalGenomeRearrangementMapEN gbni_s.gif 2013-05-07 (火) 17:30:56
IMC_O07_LocalGenomeRearrangementMapJP japan_s.gif 2013-05-07 (火) 17:31:30

O08: List of EC Numbers

wiki
IMC_ECNumberListBetweenGenomesEN? gbni_s.gif &lastmod(IMC_ECNumberListBetweenGenomesEN);
IMC_ECNumberListBetweenGenomes? japan_s.gif &lastmod(IMC_ECNumberListBetweenGenomes);

O09: Metagenome Analysis using 16SrRNA

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fileIMC_O09.en.pdf gbni_s.gif
fileIMC_O09.ja.pdf japan_s.gif
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IMC_O09_16SrRNAMetaGenomeAnalysisEN gbni_s.gif 2013-05-07 (火) 17:31:07
IMC_O09_16SrRNAMetaGenomeAnalysisJP japan_s.gif 2013-05-07 (火) 17:31:30

P: Genome Mapping

P01: EST Mapping

P02: Trace Mapping

wiki
IMC_TraceMapping?

P03: SNPマッピング

P04: アミノ酸配列マッピング

0P5: アレイプローブマッピング

  • Refer to Array Analysis

Q: タイリングアレイ解析

Q01: Tiling Array Probe設計

Q02: Probe Mapping

Q02A: Overviews on Probe Mapping

Q02B: Load Annotated Sequence File

Q02C: Probe Mapping Operation

Q02D: Probe Mapping File Saving

Q03: Array File Handling

Q03A: Loading Probe Mapped Sequence File

Q03B: Loading Expression Array Files

Q03C: Automatic Importing of Array Data

  • Launch "Batch Import"
  • Settings of "Batch Import"
  • Starting of "Batch Import"

Q03D: Array Import Error Handling

  • 不一致検出
  • エラーリストのCSVファイル出力

Q04: Arrayプロファイルレーン操作

Q04A: 発現アレイファイル読込

Q04B: プロファイルの表示・非表示切換

  • 発現プロファイル表示・非表示
  • 一時的に表示・非表示

Q04C: プロファイル表示アレイの選択

Q04D: 複数プロファイル並行表示 

Q04E: プロファイルのズーム 

Q04F: プロファイルのスケール

  • プロファイルのスケール変更
  • スケールを対数表示

Q04G: プロファイルにデータラベル表示 

Q04H: プロファイルのグラフ表示

  • プロファイルを棒グラフ表示
  • プロファイルを誤差グラフ表示
  • プロファイルを折れ線グラフ表示
  • グラフのカラー描画

Q04I: マイナス鎖の表示方法

  • マイナス鎖を下向きに表示
  • マイナス鎖のプロファイルをプラス鎖にオーバーレイ

Q04J: プロファイル印刷 

Q05: Arrayデータ補正

wiki
IMC_ArrayDataCorrection?
  • 補正設定
  • 分布表示
  • 補正実行
  • 補正結果の保存

Q06: 遺伝子レベル変換・操作

  • プローブレベルから遺伝子レベルへの変換
  • 変換集計結果のソート
  • 変換集計結果のファイル保存
  • 遺伝子レベル発現量平均値計算
  • 遺伝子レベルクラスタリング

Q07: Array間発現相関

  • 2枚のアレイ間の二次元プロット図
  • R-Iプロット図

Q08: Array間演算

  • 数値分布表示
  • 表示するプローブ範囲変更
  • Array間演算結果分布表示

Q09: Array部分ファイル作成

Q10: プロファイルからのピーク検出

R: アミノ酸配列解析

R01: アミノ酸二次構造プロファイル

R02: アミノ酸モティーフ検索

R03: アミノ酸配列マルチプルアラインメント

R04: アミノ酸配列相同性検索

R05: アミノ酸配列のゲノムへのマッピング

S: Utiliteis

S01: GenBank File Checker

S02: 圧縮形式ファイルの系統樹展開

S03: 関連サイト登録・簡易接続

S04: 最新Version確認・ダウンロード操作

S05: Lab Note

S06: Trace Chart

S07: Phylogenetic Tree

T: Tools

T01: in silico (de novo) Assembler

wiki
in silico AssemblerEN gbni_s.gif 2013-05-07 (火) 17:31:30
in silico Assembler japan_s.gif 2013-05-07 (火) 17:31:18

T02: TaxiSpider

wiki
TaxiSpiderEN? gbni_s.gif &lastmod(TaxiSpiderMapEN);
TaxiSpider japan_s.gif 2013-05-07 (火) 17:30:57

T03: iSpider

wiki
iSpiderEN? gbni_s.gif &lastmod(iSpiderEN);
iSpider japan_s.gif 2013-05-07 (火) 17:30:53

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Last-modified: 2013-08-15 (木) 14:33:19 (2079d)